A Functional Medicine Candida Overgrowth Protocol: Testing, Nutrition, and Supplements

Candida is a naturally occurring fungus that grows in and on our bodies. But when conditions allow it to grow out of control, it can lead to an imbalance known as candidiasis or candida overgrowth. This may contribute to bloating and gastrointestinal discomfort, skin rashes, frequent vaginal yeast imbalances, thrush or a white coating on the tongue, and feelings of fatigue.

Overgrowth of candida in the gastrointestinal (GI) tract is associated with an imbalance within the gut flora of bacteria, viruses, and fungi and/or issues with the immune system that allows this yeast to multiply beyond normal commensal levels. A diet that's high in sugar and processed foods is often a significant contributor.

A functional medicine approach to candida overgrowth in the gut can uncover underlying factors that allow the fungi to overgrow. This approach uses advanced lab testing like the GI-MAP, as well as diet, lifestyle, and supplements to rebalance the body. For example, focusing on non-starchy vegetables, lean protein, healthy fats, and gluten-free grains can help prevent candida overgrowth.

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What is Candida Overgrowth?

Candida albicans is a kind of yeast that's the most common in the human body. Under balanced conditions, it is part of a healthy microbiome in the gut, mouth, throat, vagina, and skin, where it exists in balance with other microbes such as bacteria, viruses, and fungi and usually does not cause any harm.

The gut mycobiome includes a variety of fungi, the most prevalent of which is candida. The mycobiome is a small but crucial component of the gut microbiome in humans, which works alongside bacteria in the gut to support host immunity and manage inflammation.

When everything is in balance, candida overgrowth is contained by a healthy immune system and balanced flora in the gut. But if candida overgrows, it can contribute to gastrointestinal discomfort, skin rashes, and frequent yeast imbalances. This can occur due to a disruption to your internal ecosystem caused by imbalanced nutrition, medications, or processes that impact the immune system and healthy balance of organisms, allowing candida to multiply.

Candida Overgrowth Symptoms

There are different symptoms of candida overgrowth depending on where in the body the imbalance occurs. Overall, some common symptoms of candida overgrowth in the gastrointestinal tract include:

• belching
• bloating
• gas
• indigestion
• fullness in the upper abdomen
• nausea
• diarrhea

Symptoms can also occur throughout the body if candida overgrowth occurs beyond the gut, including:

• red patches of skin with small, raised bumps
• itching
• burning
• white or yellow cottage cheese-like vaginal discharge
• white patches on the tongue or sores in your mouth that cause loss of taste or discomfort when eating or swallowing
• joint discomfort
• chronic fatigue

Gastrointestinal Problems

When candida overgrows in the gastrointestinal (GI) tract, it can affect the lining of your gut, potentially leading to an increased risk of leaky gut syndrome (gut permeability) and an imbalanced microbiome. This may contribute to generalized irritable bowel (IBS) symptoms, such as bloating, discomfort, constipation, and diarrhea, and, if not managed, further issues with digestion and gastrointestinal function. The excess candida can begin a fermentation process in your gut that produces gasses contributing to bloating. Fungi can ferment some carbohydrates into ethanol/alcohol and may mimic a food intolerance or sensitivity.

SIFO, or small intestinal fungal overgrowth, is one type of dysbiosis that occurs when an excess amount of fungi or yeast overgrow in the small intestine of the digestive tract. This overgrowth may contribute to gastrointestinal symptoms such as abdominal bloating and discomfort, gas, belching, diarrhea, and nausea, and over time may lead to nutrient imbalances and weight changes if not addressed.

Feelings of fatigue may occur since gut imbalances from candida overgrowth can affect the immune system and result in nutrient deficiencies in vitamin B6, essential fatty acids, and magnesium. These imbalances can contribute to inflammation throughout the body as well as nutrient imbalances and weight changes.

Autoimmunity

Since candida overgrowth may affect your gut lining, toxins, microbes, proteins, and undigested food particles can escape into your bloodstream, where your immune system may mark these as pathogens and respond to them. This can contribute to food sensitivities, immune responses on tissues, and chronic inflammation. Studies indicate that candida overgrowth is linked to Sjogren's, gastric ulcers, ulcerative colitis, and Crohn's disease.

Vaginitis

When candida overgrows in the gut, there may also be imbalances in the vaginal flora. Vaginal candidiasis may cause burning, itching, redness, and discharge from the vagina.

Skin and Nail Infections

Similarly, an imbalance in the gut microbiome may also be accompanied by an imbalance in the skin microbiome. Candida usually lives on the surface of the skin. But when candida overgrowth occurs on the skin, it can create an imbalance called cutaneous candidiasis. Since candida thrives in warm, moist environments, overgrowth often occurs between skin creases or folds like the armpit, groin, torso, or under the breasts, creating a raised, red patch with small, itchy bumps. Sometimes, the fungi can make their way beneath the skin or nail's surface and contribute to an imbalance of the nail or toenail fungus.

Oral Candidiasis (Thrush)

When candida overgrowth occurs in the mouth, it creates an imbalance that causes a white coating or sores known as thrush. This can occur in the mouth, throat, esophagus, or tongue.

Frequent Urinary Tract Infections (UTI)

UTIs are commonly caused by bacteria. But since Candida Albicans is an opportunistic fungal organism, it can overgrow in the urinary tract contributing to frequent UTIs.

Invasive Candidiasis (Systemic Candidiasis)

When an imbalance with candida spreads into the bloodstream (candidemia), a serious condition can occur throughout your body. Systemic candidiasis is most common in those with a deficiency of the immune system and can affect the blood, heart, brain, eyes, bones, and other parts of the body. Candidemia is one of the most commonly seen causes of bloodstream infections in patients who are hospitalized in the US, with emerging concerns over infections like this being caused by strains of candida auris that are resistant to many antifungal medications.

What Causes Candida Overgrowth in the GI Tract?

Several factors can make fungi more likely to overgrow in the gastrointestinal tract or other body sites. This could happen when the immune system is not functioning normally due to an illness or medication like steroids or from disruptions in the flora in the gut. When the immune system is lowered or weakened due to diseases like HIV or medicines like chemotherapy, immunosuppressants, or steroids, candida can cause overgrowth or get into the bloodstream and quickly spread throughout the body.

Fungal strains (like bacterial strains) are a normal part of the gut ecosystem as part of a diverse microbiome. Dysbiosis, or an imbalance of the good versus harmful microbes in your gut, can throw the normal balance off and allow candida to multiply quickly. This imbalance of the microbes in the gut could happen due to various different factors.

Antibiotic use can affect not only harmful bacteria but helpful bacteria as well. Low stomach acid increases the risk of fungal overgrowth since stomach acid is critical for managing bacteria and fungi before they enter the small intestine. Low stomach acid can occur from long-term use of proton-pump inhibitor (PPI) medications, age over 65, nutrient deficiencies, including protein, iron, calcium, and vitamin B12, infection with H.pylori, and atrophic gastritis. Proton pump inhibitors (PPIs) decrease the amount of acid produced and inhibit the growth of Lactobacillus species as normal flora, which can increase the risk of bacterial or fungal buildup.

A diet high in refined carbs, sugars, or excessive alcohol consumption can cause dysbiosis allowing candida to overgrow in the GI tract. In individuals with diabetes, blood sugar levels may be higher, which can dysregulate the immune system and support the growth of candida.

When the movement of food through the small intestine is slowed, it increases the risk of candida overgrowth. Some causes of slowed gastrointestinal motility include diabetes, Ehlers-Danlos syndrome, colectomy surgery that removes part of the intestines, gastroparesis, thyroid disorders, including hypothyroidism and Hashimoto's, and chronically sedentary behavior, which impairs blood flow to the digestive tract.

Inflammatory bowel disease (IBD), including Ulcerative Colitis and Crohn's disease, as well as medications used to manage this condition, can contribute to candida overgrowth. Chronic inflammation and treatments such as anti-TNFa agents may affect gastrointestinal health, which allows pathogens to penetrate the intestinal lining causing microbial imbalance like candida overgrowth.

Chronically high stress levels can also affect the immune system and disrupt the gut microbiome.

Heavy metal exposure may also play a role in candida overgrowth. Heavy metals can affect the immune system and microbiome, which allows candida to multiply. Candida can protect itself from metal exposure by gradually absorbing them into biofilms which may give it a significant advantage and allow it to become more abundant in the microbiome under these conditions.

Functional Medicine Labs to Test for Root Cause of Candida Overgrowth and Personalize Treatment

The following labs help explore the root causes of candida overgrowth:

Evaluating the Microbiome

A‍ comprehensive stool test like the GI-MAP evaluates the balance of the microbiome, including measuring levels of candida species. This test can help uncover candida albican's overgrowth and investigate possible reasons for the overgrowth, such as dysbiosis. Relevant biomarkers include Candida albicans, Candida spp., Microsporidia spp., and other fungal organisms. Retesting a few months after treatment can guide an individualized approach.

The GI-Effects Gut Pathogen Profile is an option to assess the makeup of the microbiome and receive viable options for identified imbalances. This test can help determine which approaches are most effective in addressing an individual's specific type of candida overgrowth.

Candida Testing

Alongside a stool test, additional blood and urine testing can provide a comprehensive picture of candida overgrowth in the body. Looking at IgA, IgG, and IgM reactivity to candida with the Candida Profile from Alletess Medical Laboratory can help determine if this fungus is causing an immune reaction.

Urine testing is also available to help detect invasive candidiasis. The Candida Panel from RealTime Laboratories is an at-home urine test that detects candida DNA to help identify invasive fungal imbalances.      

Heavy Metal Testing

A heavy metals profile measures any heavy metals that may have accumulated in the body and contribute to candida overgrowth and immune function.

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SIBO Testing

Since SIBO and SIFO can present with very similar symptoms and often occur together, evaluating for an overgrowth of pathogenic bacteria in the small intestine when SIFO or other forms of candida overgrowth is suspected is essential. A breath test can assess the overgrowth of bacteria that do not normally belong in the small intestine. The 3-hour SIBO assessment is a non-invasive breath test that measures hydrogen and methane to evaluate bacterial overgrowth in the small intestine.

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Small Bowel Aspirate Test

The "gold standard" for identifying SIFO is a small bowel aspirate. During an upper endoscopy, this procedure involves inserting a tubular instrument through the esophagus and stomach into a portion of the small intestines called the duodenum. From there, fluid is collected and analyzed for the presence of abnormal fungi or bacteria.

Swabs can also be taken from other sites with suspected candida imbalance for laboratory analysis.

Urinalysis

If a UTI is present, a clean catch urinalysis and a urine culture can confirm if your UTI is coming from bacteria or yeast.

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Conventional Approaches for Candida Overgrowth

Oral 'azole' antifungals like fluconazole, itraconazole, or posaconazole are the most common physician-prescribed drugs to manage candida imbalances. Fluconazole works by inhibiting the Cytochrome p450 enzyme, leading to the arrest of fungal growth and creating holes in the fungal cell membrane, causing the cells to become permeable and die.

Candida imbalances are also managed with other drugs such as caspofungin, terbinafine, and amphotericin B. Combining one of these antifungals with an -azole drug has been shown to have increased efficacy.

Functional Medicine Approach for GI Candida Overgrowth

A functional medicine approach explores and addresses underlying root causes to manage candida overgrowth in the gastrointestinal tract. Approaches vary depending on many individual factors. Optimizing nutrition, utilizing natural therapies, and modifying your lifestyle can help support a balanced environment in the gut.

Therapeutic Diet and Nutrition Considerations for Candida Overgrowth

A dietary approach to candida overgrowth includes focusing on low-sugar fruits, non-starchy vegetables, non-glutinous grains, some fermented foods, and dairy products. The Anti-Candida, Low FODMAP, anti-inflammatory Mediterranean diet, and elemental diets may be used in some cases.

Blood sugar dysregulation can set the stage for candida to multiply. This typically occurs from high carbohydrate diets, especially in those with certain underlying conditions such as diabetes and metabolic syndrome. To address this, a therapeutic diet for candida overgrowth often avoids sugars, including honey and artificial sweeteners, high fructose corn syrup, alcohol, and starchy carbohydrates like potatoes.

Avoiding excessive inflammation is also key to supporting gut health and limiting candida overgrowth. An individualized anti-inflammatory diet should avoid foods to which one is allergic or sensitive, as well as processed meats, soda, other sweetened beverages, and processed oils.

Anti-Candida Diet

An anti-Candida Diet emphasizes low-sugar, anti-inflammatory foods to promote a healthy microbiome, manage inflammation, support the immune system, and stabilize blood sugar levels. This diet is designed to help diminish the overgrowth of yeast and bring the microbiome back into balance.

Low FODMAP Diet

A low FODMAP (standing for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols) diet limits short-chain carbohydrates, which can be challenging to digest and feed yeast and bacteria in the small intestine. Eliminating foods like beans and legumes, corn, seeds and nuts, and cruciferous vegetables that can irritate the stomach or cause delayed emptying can reduce symptoms for some. Following a gluten-free or grain-free diet can also improve symptoms of candida overgrowth.

Mediterranean Diet

A Mediterranean diet, emphasizing citrus fruits, vegetables, legumes, and complex carbohydrates with moderate fish and olive oil, helps balance inflammation and promotes gut health to help manage and prevent candida overgrowth.

Elemental Diet

An elemental diet is a liquid meal replacement formula that provides a complete nutritional profile broken down into its most "elemental" forms. Fat, proteins, and carbohydrates are broken down into amino acids, short-chain triglycerides, short-chain maltodextrins, and vitamins, minerals, and electrolytes in a comprehensive "predigested" formula easily absorbed by the digestive tract. Fiber is generally excluded as it can feed bacteria that have relocated into the small intestines. An elemental diet may be used to address SIBO or SIFO by replacing other food for two to three weeks to manage the yeast or bacteria in the small intestine while still adequately nourishing the body.

Rebalance the Microbiome

Restoring equilibrium in the gut microbiota by eating a variety of whole foods and incorporating probiotic-rich foods like sauerkraut and kimchi that contain naturally-occurring probiotics and prebiotic-rich foods like artichokes, garlic, and beans that nourish healthy bacteria is critical for helping to bring the microbiome back into balance and managing excess inflammation.

Supplements Protocol for Candida Overgrowth

In addition to making dietary modifications, some supplements can help your body manage candida overgrowth. As an alternative to or a complement to conventional antifungals, probiotics and herbal antimicrobials like caprylic acid, oregano oil, garlic, and berberine are sometimes used for antifungal support. This approach to addressing candida overgrowth in the gastrointestinal tract involves reducing candida while supporting the beneficial bacteria that usually keep them in check.

Supplement protocols for candida overgrowth should be individualized for the specific patient, type of imbalance, and other contributing factors. The GI Effects comprehensive stool test can help guide a personalized approach by showing which prescriptive and natural agents are effective at managing the growth of the candida specific to the patient's microbiome.

Probiotics

Probiotics are beneficial live microorganisms (e.g., bacteria, yeasts) that help to replenish and balance the microbiome. Probiotics are naturally found in several foods, including yogurt and other fermented foods, such as kombucha, kimchi, and sauerkraut, and are also available in supplement form.

Probiotics, particularly Lactobacilli strains, have been shown to support balanced candida levels in different organ systems of the human body. Lactobacillus acidophilus produces lactic acid as a byproduct of its metabolism, which helps to regulate the acidity in your gut, support your immune system, and significantly inhibit the rate at which candida grows. For example, older adults with thrush who took lozenges containing two strains of the probiotic Lactobacillus reuteri significantly reduced candida in their mouths. Probiotics can also help minimize candida imbalance incidence in critically ill patients. A comprehensive stool test can help identify which probiotics your gut microbiome is deficient in and guide specific support.

Probiotics can be taken throughout the antifungal support and should be taken with food, 2-3 hours apart from antimicrobials.

Furthermore, a probiotic containing the beneficial yeast Saccharomyces boulardii can help prevent dysbiosis like SIFO when taking antibiotics. S. boulardii supports balanced candida levels in two ways. It breaks down the protective biofilm that candida hides in to grow without the immune system interfering and crowds out candida in the mycobiome.

Dose: 8-15+ billion colony-forming units of bacteria containing a variety of strains, including L. acidophilus and L. paracasei tailored to individual needs

Duration: 4+ weeks

Caprylic Acid

Caprylic acid is a medium-chain fatty acid that is naturally found in mammalian breast milk and coconut oil. It has properties that help break down and manage candida by penetrating its cell membranes and biofilms. Caprylic acid was found to be a superior and more cost-effective option for reducing candida overgrowth symptoms when compared to some prescription antifungals.

Dose: 500 to 1,000 milligrams three times a day

Duration: 3-4 months

Oregano

Oregano oil (Origanum vulgare) is another potent natural option that helps manage candida. It may be used to address candida imbalances, including those caused by C. albicans, C. glabrata, and C. parapsilosis.

Candida can form biofilms in the intestines, a protective mechanism they use to hide from the immune system while they continue to multiply. Studies have found that oregano oil helps manage candida overgrowth by breaking down the biofilm that develops over the mucosal and epithelial surface of the intestinal tract. Oregano selectively targets pathogenic fungi and bacteria while leaving Lactobacilli and Bifidobacterium of the healthy microbiome alone to help restore balance in the gut.

Oregano oil can also be taken in combination with other herbal options in preparations like Candibactin to support intestinal microbial balance. Under the direction of your provider, a binder like Metal-X Synergy™ or another binding agent may be added to regimens containing antifungals like oregano oil for potential die-off reactions.

Dose: 2-6 drops of organic oregano oil in a small cup of water twice a day or 1-2 softgels of oregano oil or as part of combinations like Candibactin taken in one to three doses per day

Duration: 10 days

Garlic

The benefits of garlic are largely due to allicin. Garlic oil disrupts Candida albicans largely by inhibiting thiol-containing amino acids and proteins, therefore interfering with cell metabolism and also inhibiting the growth of certain bacteria like Bacillus subtilis, Escherichia coli, and Staphylococcus aureus to help balance the microbiome. Human cells contain glutathione which binds to allicin, preventing cell damage. While candida lacks glutathione, allicin acts as a selective anti-candida support.

Garlic tablets have been shown to reduce clinical symptoms associated with candida vaginitis to a similar extent as fluconazole.

Dose: 1,500 mg daily (500 mg tablets three times a day)

Duration: 7+ days

Berberine

Berberine is found in plants such as goldenseal, Oregon grape, tree turmeric, and barberry. Berberine has broad activity and supports yeast balance by affecting the cell membrane. Berberine can also help support intestinal permeability with its antioxidant, anti-inflammatory, and mucosal healing effects.

Studies show that berberine is effective at supporting fluconazole-resistant strains of candida. Through its impact on the microbiome, it can also help to stabilize blood sugar levels, reducing the risk of candida overgrowth.

Berberine has a short half-life, so it should be taken three times a day to maintain blood levels.

Dose: 200-500mg three times per day

Duration: 6 weeks

Combination Formulas

Many of these herbal options and other phytonutrients work synergistically in combination with herbal formulas to support healthy microbial balance. Candibactin-AR® and Candibactin-BR® and FC Cidal™ and Dysbiocide® are combination herbal formulas that are proven effective in addressing SIBO when administered daily for four weeks. They may also help with an overgrowth of candida in the gut. Another combination herbal option to support microbial balance in the gut is GI Microb-X® which contains berberine and caprylic acid to support yeast balance and biofilms, in addition to several other botanicals to help normalize the microbiome.

Dose: 1 sofgel three times per day or Candibactin, 1 capsule two times per day of FC-Cidal,™ or 2 capsules GI Microb-X® three times per day taken between meals, away from probiotics or as directed

Duration: 4-6 weeks

When to Retest Labs

Depending on the overall picture and approach, reviewing clinical symptoms or repeat laboratory testing after 6-8 weeks can determine whether the approach has been sufficient or needs to be continued or modified. For example, repeating comprehensive GI stool testing a few months into the approach allows for any modification that may be needed to move toward greater microbial balance.

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Summary

Candida is a naturally occurring fungus that grows in and on your body. When conditions allow it to grow out of control, it can lead to an imbalance known as candidiasis or candida overgrowth. Overgrowth of candida occurs in the gastrointestinal tract when there are certain issues with the function of the immune system and imbalances in the normal flora of bacteria, viruses, and fungi. This can occur after taking antibiotics, PPIs, or steroids, with prolonged high intake of processed sugars or alcohol, or from underlying conditions that affect the immune system like diabetes or HIV infection.

The proliferation of candida in the gastrointestinal tract can cause gas, bloating, nausea, and diarrhea, along with nutrient imbalances and weight changes if not managed. Functional medicine testing to look at microbes in the gastrointestinal tract and measure for immune responses to candida can help narrow in on the imbalance.

A functional medicine approach explores underlying root causes to manage candida overgrowth in the gastrointestinal tract. Approaches vary depending on many individual factors but often incorporate optimizing nutrition and targeted antifungal support to manage and prevent candida overgrowth. A diet focused on non-starchy vegetables, some low-sugar fruits, non-gluten grains, and fermented foods may help reduce the overgrowth of yeast and bring the microbiome back into balance. Prescription or herbal antifungals are sometimes used to help manage the growth of fungi in the bowels. Probiotics and herbal antimicrobials like caprylic acid, oregano oil, garlic, and berberine are used to reduce candida while also supporting the friendly bacteria that usually keep them in check.